Contacts of the helix formed by residues 83 - 87 (chain 2) in PDB entry 1QJX
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 83 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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822 LEU* 1.3 83.4 - - + +
842 ASP* 1.3 65.7 + - - +
852 ALA 3.3 2.9 - - - -
862 LEU* 2.8 18.4 + - + +
872 LYS 3.4 6.2 + - - -
922 PHE* 4.1 13.9 - - + -
962 MET* 4.1 7.6 - - + +
1062 TYR* 3.5 17.0 - - + +
2132 MET* 3.5 50.0 - - + +
2162 HIS 3.7 8.5 - - - +
2172 ASN* 3.6 6.7 - - - +
2182 ASN* 3.6 19.3 - - - +
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Residues in contact with ASP 84 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812 LYS* 3.2 11.4 + - + +
832 PRO* 1.3 76.7 - - - +
852 ALA* 1.3 63.8 + - - +
862 LEU 2.9 1.9 + - - -
872 LYS* 2.8 58.7 + - - +
962 MET* 4.8 4.3 - - - -
1472 THR 4.3 0.2 - - - +
1482 HIS* 3.2 30.8 - - + +
1492 PRO* 3.3 5.2 - - - +
1502 GLY* 2.7 28.6 + - - +
2132 MET 5.1 1.3 + - - +
2172 ASN* 3.3 25.8 + - - +
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Residues in contact with ALA 85 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662 LEU* 4.3 12.3 - - + +
802 TRP* 4.1 23.6 - - + -
812 LYS 2.7 20.1 + - - +
822 LEU* 4.2 12.6 - - + -
832 PRO 3.1 0.4 + - - -
842 ASP* 1.3 73.3 - - - +
862 LEU* 1.3 63.7 + - + +
872 LYS* 3.5 1.0 + - - +
882 ASP 5.1 1.0 + - - -
892 MET* 4.4 4.2 - - - +
1502 GLY 3.7 21.5 - - - +
1512 GLU* 3.5 22.8 + - - +
2442 ILE* 5.1 0.2 - - + -
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Residues in contact with LEU 86 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642 TYR* 4.0 17.9 - - + -
662 LEU* 4.1 13.5 - - + -
822 LEU* 4.2 9.9 - - + -
832 PRO 2.8 10.4 + - - +
852 ALA* 1.3 81.7 - - - +
872 LYS* 1.3 58.6 + - - +
882 ASP 2.9 12.1 + - - -
892 MET* 2.9 34.3 + - + +
922 PHE* 3.8 17.4 - - + -
932 GLY* 3.8 8.1 - - - -
1062 TYR* 3.9 28.0 - - + -
2442 ILE* 4.1 21.5 - - + -
2462 PRO* 4.0 21.5 - - + -
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Residues in contact with LYS 87 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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832 PRO 3.4 2.6 + - - -
842 ASP* 2.8 37.7 + - - +
852 ALA 5.1 0.4 - - - +
862 LEU* 1.3 75.4 - - - +
882 ASP* 1.3 65.4 + - + +
892 MET 3.5 0.7 - - - -
932 GLY* 3.4 12.3 - - - -
962 MET* 3.7 24.9 - - + -
972 PHE* 3.2 41.2 - - + -
1482 HIS* 2.9 26.3 + - - +
1492 PRO 4.4 0.4 - - - -
1502 GLY* 3.6 17.4 - - - +
1512 GLU 5.8 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il